Variant report

Variant	rs1325659
Chromosome Location	chr13:50161042-50161043
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr13:50160917-50161956	IMR90	lung:	n/a	n/a
2	STAT3	chr13:50160886-50161761	MCF10A-Er-Src	breast:	n/a	n/a
3	FOXA1	chr13:50160755-50162015	HepG2	liver:	n/a	chr13:50160757-50160769 chr13:50161818-50161830
4	FOXA1	chr13:50160866-50161198	HepG2	liver:	n/a	n/a
5	STAT3	chr13:50160985-50161761	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr13:50160738-50161761	MCF10A-Er-Src	breast:	n/a	n/a
7	FOXA1	chr13:50160826-50161132	HepG2	liver:	n/a	n/a
8	FOXA2	chr13:50160879-50161194	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:50087217..50089138-chr13:50160277..50162233,2	MCF-7	breast:
2	chr13:50016992..50019784-chr13:50159235..50161344,2	K562	blood:
3	chr13:50068906..50071236-chr13:50159028..50161203,3	MCF-7	breast:
4	chr13:50158705..50160311-chr13:50160787..50163577,2	K562	blood:
5	chr13:50016508..50019619-chr13:50158297..50162493,5	MCF-7	breast:
6	chr13:50018091..50020783-chr13:50160403..50162609,2	MCF-7	breast:
7	chr13:50091935..50095583-chr13:50159811..50161648,3	MCF-7	breast:

No data

Variant related genes	Relation type
RCBTB1	TF binding region
ENSG00000102547	Chromatin interaction
ENSG00000136147	Chromatin interaction
ENSG00000136169	Chromatin interaction
ENSG00000136144	Chromatin interaction
ENSG00000215462	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12429081	0.91[AFR][1000 genomes]
rs13378867	0.86[AFR][1000 genomes]
rs17073188	0.90[JPT][hapmap]
rs1853829	0.90[AFR][1000 genomes]
rs2407795	0.83[ASN][1000 genomes]
rs35472053	0.82[AFR][1000 genomes]
rs3851161	0.87[AFR][1000 genomes]
rs4942853	0.90[AFR][1000 genomes]
rs4942856	0.83[ASN][1000 genomes]
rs61961441	0.91[AFR][1000 genomes]
rs7321549	0.91[AFR][1000 genomes]
rs7332010	0.94[ASW][hapmap];0.93[LWK][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes]
rs7332641	0.91[AFR][1000 genomes]
rs7336812	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.86[ASN][1000 genomes]
rs7995979	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9316461	0.91[AFR][1000 genomes]
rs9316467	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9591285	0.82[AFR][1000 genomes]
rs9670479	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1036135	chr13:50071310-50183103	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv541770	chr13:50071310-50183103	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1054965	chr13:50102730-50251347	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv541771	chr13:50102730-50251347	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv2763020	chr13:50105055-50192259	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv561616	chr13:50120435-50190246	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	nsv949162	chr13:50120985-50195882	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv1046912	chr13:50122840-50189313	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv1043902	chr13:50122840-50189999	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
13	esv2761789	chr13:50122852-50185910	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
14	nsv455883	chr13:50124621-50185204	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
15	nsv561617	chr13:50124621-50185204	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
16	nsv1043697	chr13:50129199-50249241	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
17	esv2752657	chr13:50144995-50244150	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1325659	ARL11	Cis_1M	lymphoblastoid	RTeQTL
rs1325659	RCBTB1	cis	cerebellum	SCAN
rs1325659	ARL11	cis	lymphoblastoid	seeQTL
rs1325659	RCBTB1	cis	Nerve Tibial	GTEx
rs1325659	RCBTB1	cis	Whole Blood	GTEx
rs1325659	RCBTB1	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50160400-50161200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr13:50160400-50161400	Weak transcription	HSMM	muscle
3	chr13:50160400-50161800	Enhancers	Muscle Satellite Cultured Cells	--
4	chr13:50160400-50161800	Flanking Active TSS	HepG2	liver
5	chr13:50160400-50161800	Enhancers	HSMMtube	muscle
6	chr13:50160400-50161800	Enhancers	NHLF	lung
7	chr13:50160400-50161800	Enhancers	Osteobl	bone
8	chr13:50160400-50162000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr13:50160400-50162200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr13:50160600-50161400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr13:50160600-50161400	Enhancers	Brain Anterior Caudate	brain
12	chr13:50160600-50161600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr13:50160600-50161600	Enhancers	Liver	Liver
14	chr13:50160600-50161600	Enhancers	A549	lung
15	chr13:50160600-50161600	Weak transcription	K562	blood
16	chr13:50160600-50161800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr13:50160600-50161800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr13:50160600-50161800	Enhancers	HUVEC	blood vessel
19	chr13:50160600-50162000	Enhancers	Hela-S3	cervix
20	chr13:50160600-50162400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr13:50160600-50162400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr13:50160600-50162400	Enhancers	HMEC	breast
23	chr13:50160600-50162600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr13:50160600-50169200	Weak transcription	Esophagus	oesophagus
25	chr13:50160800-50161200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr13:50160800-50161400	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr13:50160800-50161400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr13:50160800-50161400	Weak transcription	Psoas Muscle	Psoas
29	chr13:50161000-50161600	Weak transcription	Fetal Heart	heart
30	chr13:50161000-50161800	Enhancers	NH-A	brain
31	chr13:50161000-50161800	Flanking Active TSS	NHEK	skin

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